Gene Expression Profiles Of Tissues Research Articles

Universal Nature of Drug Treatment Responses in Drug-Tissue-Wide Model-Animal Experiments Using Tensor Decomposition-Based Unsupervised Feature Extraction.

Gene expression profiles of tissues treated with drugs have recently been used to infer clinical outcomes. Although this method is often successful from the application point of view, gene expression altered by drugs is rarely analyzed in detail, because of the extremely large number of genes involved. Here, we applied tensor decomposition (TD)-based unsupervised feature extraction (FE) to the gene expression profiles of 24 mouse tissues treated with 15 drugs. TD-based unsupervised FE enabled identification of the common effects of 15 drugs including an interesting universal feature: these drugs affect genes in a gene-group-wide manner and were dependent on three tissue types (neuronal, muscular, and gastroenterological). For each tissue group, TD-based unsupervised FE enabled identification of a few tens to a few hundreds of genes affected by the drug treatment. These genes are distinctly expressed between drug treatments and controls as well as between tissues in individual tissue groups and other tissues. We also validated the assignment of genes to individual tissue groups using multiple enrichment analyses. We conclude that TD-based unsupervised FE is a promising method for integrated analysis of gene expression profiles from multiple tissues treated with multiple drugs in a completely unsupervised manner.

Poplar Propolis Ethanolic Extract Reduces Body Weight Gain and Glucose Metabolism Disruption in High-Fat Diet-Fed Mice.

Current evidence supports the beneficial effect of polyphenols on the management of obesity and associated comorbidities. This is the case for propolis, a polyphenol-rich substance produced by bees. The aim of the present study is to evaluate the effect of a poplar propolis ethanolic extract (PPEE) on obesity and glucose homeostasis, and to unveil its putative molecular mechanisms of action. Male high-fat (HF) diet-fed mice are administered PPEE for 12 weeks. PPEE supplementation reduces the HF-mediated adiposity index, adipocyte hypertrophy, and body weight gain. It also improves HOMA-IR and fasting glucose levels. Gene expression profiling of adipose tissue (AT) shows an induction of mRNA related to lipid catabolism and mitochondrial biogenesis and inhibition of mRNA coding for inflammatory markers. Interestingly, several Nrf2-target genes are induced in AT following administration of PPEE. The ability of PPEE to induce the expression of Nrf2-target genes is studied in adipocytes. PPEE is found to transactivate the Nrf2 response element and the Nrf2 DNA-binding, suggesting that part of the effect of PPEE can be mediated by Nrf2. PPEE supplementation may represent an interesting preventive strategy to tackle the onset of obesity and associated metabolic disorders.

Gene expression profiles during postnatal development of the liver and pancreas in giant pandas

Giant pandas are unique Carnivora with a strict bamboo diet. To investigate the molecular mechanism of giant panda nutrient metabolism from newborn to adult, the gene expression profiles of giant panda liver and pancreas tissues collected from three important feeding stages were investigated using RNA-seq. We found a total of 3,211 hepatic and 3,343 pancreatic differentially expressed genes (DEGs) from three comparisons between suckling and no feeding, adult and no feeding, and adult and suckling groups. Few differences in gene-expression profiles were exhibited between no feeding and suckling groups in both tissues. GO and KEGG analyses were performed to further understand the biological functions of the DEGs. In both the liver and pancreas, genes related mainly to cell cycle processes were highly up-regulated in newborn samples whereas genes related to metabolism and immunity were up-regulated in adult giant pandas. The high expression of metabolism-related genes in adult samples probably helps to fulfill the metabolic function requirements of the liver and pancreas. In contrast, several vital genes involved in cholesterol metabolism and protein digestion and absorption were over-expressed in newborn samples. This may indicate the importance of cholesterol metabolism and protein digestion and absorption processes in giant panda infancy.

Transcriptomics Study to Determine the Molecular Mechanism by which sIL-13Rα2-Fc Inhibits Caudal Intervertebral Disc Degeneration in Rats.

Background Intervertebral disc degeneration is related to tissue fibrosis. ADAMTS can degrade the important components of the ECM during the process of intervertebral disc degeneration, ultimately resulting in the loss of intervertebral disc function. sIL-13Rα2-Fc can inhibit fibrosis and slow down the degeneration process, but the mechanism involved remains unclear. Objective To determine the mechanism by which sIL-13Rα2-Fc inhibits ECM degradation and reduces intervertebral disc tissue fibrosis using a transcriptomics analysis. Methods A rat model of caudal intervertebral disc degeneration was established, and Sirius red staining was used to observe the pathological changes in the caudal intervertebral disc. Transcriptome sequencing was employed to assess the gene expression profiles of the intervertebral disc tissues in the model group and the sIL-13Rα2-Fc-treated group. Differentially expressed genes were identified and analyzed using GO annotation and KEGG pathway analyses. Real-time fluorescence quantitative PCR was used to verify the expression levels of candidate genes. The levels of GAG and HA were quantitatively assessed by ELISA, and the levels of collagen I and collagen II were analyzed by western blotting. Results Sirius red staining showed that in the model group, the annulus fibrosus was disordered, the number of breaks increased, and the type I collagen protein levels increased, whereas in the sIL-13Rα2-Fc group, the annulus fibrosus was ordered, the number of breaks decreased, and the type II collagen protein levels increased. In comparison with the model group, we identified 58 differentially expressed genes in the sIL-13Rα2-Fc group, and these were involved in 35 signaling pathways. Compared with those in the model group, the mRNA expression levels of Rnux1, Sod2, and Tnfaip6 in the IL-13Rα2-Fc group were upregulated, and the mRNA expression levels of Aldh3a1, Galnt3, Fgf1, Celsr1, and Adamts8 were downregulated; these results were verified by real-time fluorescence quantitative PCR. TIMP-1 (an ADAMTS inhibitor) and TIMP-1 combined with the sIL-13Rα2-Fc intervention increased the levels of GAG and HA, inhibited the expression of type I collagen, and promoted the expression of type II collagen. Conclusion Adamts8 may participate in the degradation of ECM components such as GAG and HA and lead to an imbalance in the ECM of the intervertebral disc, resulting in intervertebral disc degeneration. sIL-13Rα2-Fc promoted anabolism of the ECM and increased the levels of ECM components by inhibiting the expression of Adamts8, thus maintaining the dynamic equilibrium of the ECM and ultimately delaying intervertebral disc degeneration.

Abstract 50: Differences in gene-expression profiles in breast cancer between African and European-ancestry women

Abstract Background: African American (AA) women suffer from higher incidence of some forms of breast cancer and higher overall mortality than European American (EA) women. Methods: To investigate the biological basis for the racial difference in breast cancer, we compared gene expression profiles in breast cancer tissues using RNA sequencing data derived from 260 AA and 155 EA women who are participants of the Southern Community Cohort Study (SCCS) and were diagnosed with breast cancer during the cohort follow-up. Genes differentially expressed between AA and EA breast cancer patients were identified using linear regression models thresholded at false discovery rate (FDR) < 0.01. Covariates adjusted in the analysis include age at diagnosis, PAM50 subtypes, TNM stages, probabilistic estimation of expression residuals (PEER) factors, and test batch. Penalized logistic regression via ridge regularization was used to avoid overfitting and overcome the potential problem of multicollinearity by shrinking the model coefficients in building the race-specific gene expression signature. Gene expression and clinical data of 180 AA and 838 EA breast cancer patients from the Cancer Genome Atlas (TCGA) were used for external validation of the gene signature. Penalized Cox regression via elastic net was used to identify a subset of the race-differentiated genes that are associated with breast cancer survival. Results: We identified 59 genes (54 protein-coding genes and 5 long intergenic non-coding RNAs) that were differentially expressed between EA and AA with an FDR adjusted p-value < 0.01. The top three identified genes were IL20A (OMIM 605620), MARCO (OMIM 604870), and BTN3A1 (OMIM 613593), all involved in immune-related pathways. All 59 genes were included in constructing the race-differentiated gene signature. A subset of 30 racial-differentiated genes were found significantly associated with overall breast cancer survival. We externally validated our 59-gene signature by fitting the model to TCGA data and evaluated the prediction performance of the gene signature in terms of both discrimination and calibration. The C-statistic was 0.81, indicating high discriminative ability in distinguishing AA and EA breast cancer patients. The Brier score, which measures disagreement between the observed outcome and a prediction, was 0.064, indicating high reliability and prediction accuracy. Conclusion: These findings provide insights into the biological differences in tumors and the survival disparity between AA and EA breast cancer patients. Citation Format: Jie Ping, Xingyi Guo, Fei Ye, Jirong Long, Loren Lipworth, Qiuyin Cai, William J. Blot, Xiao-ou Shu, Wei Zheng. Differences in gene-expression profiles in breast cancer between African and European-ancestry women [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 50.

Abstract 6637: Inhibition of FGFR signaling by lenvatinib activates tumor interferon gamma signaling pathway and potentiates antitumor activity of anti-PD-1 antibody

Abstract Background: Lenvatinib mesilate (LEN) is an oral multiple receptor tyrosine kinase (RTK) inhibitor that selectively inhibits the kinase activity of VEGFR1-3, in addition to other proangiogenic and oncogenic pathway-related RTKs including FGFR1-4; PDGFRα; KIT; and RET. To improve the efficacy of immune checkpoint inhibitors (ICI), combination treatments of ICI plus anti-angiogenic inhibitors are currently under investigation. Lenvatinib plus pembrolizumab is approved for 2nd line treatment of advanced endometrial carcinoma that is not microsatellite instability-high or mismatch repair deficient in the US, and several Ph3 clinical trials with this combination are ongoing. Immunosuppressive roles of VEGF in tumor microenvironment have been well studied; however, immunomodulatory effects of FGFR signaling and the effect of FGFR inhibition on antitumor activity of anti-PD-1 antibody (PD-1 Ab) are still largely unknown. In this study, we investigated mechanism of action underlying the activity of LEN and PD-1 blockade in syngeneic mouse renal cell carcinoma (RCC) model. We also explored the relationship between FGFR signaling and interferon (IFN) γ signaling pathway in cancer cells, and examined whether LEN has an impact on IFNγ pathway by FGFR inhibition. Methods: We examined antitumor activity of combination treatment of LEN at 10 mg/kg (po, qd) plus PD-1 Ab at 10 mg/kg (ip, twice weekly) and VEGF-selective inhibitor axitinib (Axi) at 10 mg/kg (po, bid) plus PD-1 Ab in the RAG (murine RCC cell) subcutaneous tumor model. Gene expression profile in tumor tissues or cultured cells was analyzed by qRT-PCR or RNA seq. FGFR and IFNγ signaling pathways and their downstream molecules in tumor tissues and cultured cells were analyzed by western blot (WB) and immunofluorescence (IF). Results: In the RAG model, the combination of LEN and PD-1 Ab showed greater tumor response than each single treatment and Axi plus PD-1 Ab combination. In the tumors, WB analysis revealed LEN treatment increased STAT1 phosphorylation and PD-L1 expression and decreased the expression of SOCS1, a suppressor molecule of JAK-STAT signaling. Increased expression of PD-L1 was also observed in the tumors by IF analysis. WB and qRT-PCR analyses elucidated that activation of FGFR signaling pathway inhibited the induction of B2M, PD-L1 and CXCL10 expression in RAG cells and human cancer cell lines. Inhibition of FGFR by LEN treatment reactivated the IFNγ signaling pathway. Conclusion: Dual inhibition of VEGFR and FGFR signaling by LEN may exert the greater antitumor activity via activation of IFNγ pathway compared with single inhibition of VEGFR signaling in combination with PD-1 Ab. These results provide one of unique mechanisms of antitumor activity of LEN as VEGFR and FGFR inhibitor in combination with PD-1 blockade in preclinical models. Citation Format: Yusuke Adachi, Hiroshi Kamiyama, Kenji Ichikawa, Yoichi Ozawa, Sayo Fukushima, Satoshi Goda, Shogo Yamaguchi, Masahiro Matsuki, Saori Watanabe Miyano, Akira Yokoi, Yu Kato, Yasuhiro Funahashi. Inhibition of FGFR signaling by lenvatinib activates tumor interferon gamma signaling pathway and potentiates antitumor activity of anti-PD-1 antibody [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6637.

Genome-wide identification and analysis of AP2/ERF transcription factors related to camptothecin biosynthesis in Camptotheca acuminata.

Camptotheca acuminata produces camptothecin (CPT), a monoterpene indole alkaloid (MIA) that is widely used in the treatment of lung, colorectal, cervical, and ovarian cancers. Its biosynthesis pathway has attracted significant attention, but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors (TFs) remains unclear. In this study, a systematic analysis of the AP2/ERF TFs family in C. acuminata was performed, including phylogeny, gene structure, conserved motifs, and gene expression profiles in different tissues and organs (immature bark, cotyledons, young flower, immature fruit, mature fruit, mature leaf, roots, upper stem, and lower stem) of C. acuminata. A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (26 genes), DREB (61 genes), ERF (92 genes), RAV (18 genes), and Soloist (one gene). The combination of gene expression patterns in different C. acuminata tissues and organs, the phylogenetic tree, the co-expression analysis with biosynthetic genes, and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C. acuminata might be involved in CPT synthesis regulation, which exhibit relatively high expression levels in the upper stem or immature bark. Among these, four genes (CacAP2/ERF123, CacAP2/ERF125, CacAP2/ERF126, and CacAP2/ERF127) belong to the ERF-B2 subgroup; two genes (CacAP2/ERF149 and CacAP2/ERF152) belong to the ERF-B3 subgroup; and two more genes (CacAP2/ERF095 and CacAP2/ERF096) belong to the DREB-A6 subgroup. These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C. acuminata.

The Selective Peroxisome Proliferator-Activated Receptor Gamma Modulator CHS-131 Improves Liver Histopathology and Metabolism in a Mouse Model of Obesity and Nonalcoholic Steatohepatitis.

CHS‐131 is a selective peroxisome proliferator‐activated receptor gamma modulator with antidiabetic effects and less fluid retention and weight gain compared to thiazolidinediones in phase II clinical trials. We investigated the effects of CHS‐131 on metabolic parameters and liver histopathology in a diet‐induced obese (DIO) and biopsy‐confirmed mouse model of nonalcoholic steatohepatitis (NASH). Male C57BL/6JRj mice were fed the amylin liver NASH diet (40% fat with trans‐fat, 20% fructose, and 2% cholesterol). After 36 weeks, only animals with biopsy‐confirmed steatosis and fibrosis were included and stratified into treatment groups (n = 12‐13) to receive for the next 12 weeks (1) low‐dose CHS‐131 (10 mg/kg), (2) high‐dose CHS‐131 (30 mg/kg), or (3) vehicle. Metabolic parameters, liver pathology, metabolomics/lipidomics, markers of liver function and liver, and subcutaneous and visceral adipose tissue gene expression profiles were assessed. CHS‐131 did not affect body weight, fat mass, lean mass, water mass, or food intake in DIO‐NASH mice with fibrosis. CHS‐131 improved fasting insulin levels and insulin sensitivity as assessed by the intraperitoneal insulin tolerance test. CHS‐131 improved total plasma cholesterol, triglycerides, alanine aminotransferase, and aspartate aminotransferase and increased plasma adiponectin levels. CHS‐131 (high dose) improved liver histology and markers of hepatic fibrosis. DIO‐NASH mice treated with CHS‐131 demonstrated a hepatic shift to diacylglycerols and triacylglycerols with a lower number of carbons, increased expression of genes stimulating fatty acid oxidation and browning, and decreased expression of genes promoting fatty acid synthesis, triglyceride synthesis, and inflammation in adipose tissue. Conclusion: CHS‐131 improves liver histology in a DIO and biopsy‐confirmed mouse model of NASH by altering the hepatic lipidome, reducing insulin resistance, and improving lipid metabolism and inflammation in adipose tissue.

Transcriptome analysis provides insights into the effects of myo-inositol on the turbot Scophthalmus maximus

Myo-inositol is an essential vitamin for most animals, and it can modulate multiple physiological functions. In this study, we performed transcriptome gene expression profiling of gill tissue from turbot Scophthalmus maximus fed different concentrations of myo-inositol (0, 300, 600, 900, 1200 mg/kg). Results of expression tendency analysis, Weighted Gene Co-Expression Network Analysis (WGCNA), integrated transcriptome analyses, and KEGG annotation analysis of all differentially expressed genes (DEGs) demonstrated that the cytokine-cytokine receptor interaction played a core role in effects of myo-inositol on turbot, which was followed by the Jak-STAT signaling pathway. The results of qRT-PCR also showed myo-inositol mediated the gene expression of the cytokine-cytokine receptor interaction and the Jak-STAT signaling pathway in turbot. The ELISA assay indicated that myo-inositol affected the concentration change of interleukins (IL-2 and IL-10). Consequently, the interleukins associated with immune functions in the cytokine-cytokine receptor interaction played a core role in the effects of myo-inositol on turbot, which was followed by the Jak-STAT signaling pathway. Additionally, 10 hub genes associated with myo-inositol-traits were identified via WGCNA.

Computational Identification of Tumor Suppressor Genes Based on Gene Expression Profiles in Normal and Cancerous Gastrointestinal Tissues.

Cancer prevails in various gastrointestinal (GI) organs, such as esophagus, stomach, and colon. However, the small intestine has an extremely low cancer risk. It is interesting to investigate the molecular cues that could explain the significant difference in cancer incidence rates among different GI tissues. Using several large-scale normal and cancer tissue genomics datasets, we compared the gene expression profiling between small intestine and other GI tissues and between GI cancers and normal tissues. We identified 17 tumor suppressor genes (TSGs) which showed significantly higher expression levels in small intestine than in other GI tissues and significantly lower expression levels in GI cancers than in normal tissues. These TSGs were mainly involved in metabolism, immune, and cell growth signaling-associated pathways. Many TSGs had a positive expression correlation with survival prognosis in various cancers, confirming their tumor suppressive function. We demonstrated that the downregulation of many TSGs was associated with their hypermethylation in cancer. Moreover, we showed that the expression of many TSGs inversely correlated with tumor purity and positively correlated with antitumor immune response in various cancers, suggesting that these TSGs may exert their tumor suppressive function by promoting antitumor immunity. Furthermore, we identified a transcriptional regulatory network of the TSGs and their master transcriptional regulators (MTRs). Many of MTRs have been recognized as tumor suppressors, such as HNF4A, ZBTB7A, p53, and RUNX3. The TSGs could provide new molecular cues associated with tumorigenesis and tumor development and have potential clinical implications for cancer diagnosis, prognosis, and treatment.

Tauopathy in the young autistic brain: novel biomarker and therapeutic target

Given our recent discovery of somatic mutations in autism spectrum disorder (ASD)/intellectual disability (ID) genes in postmortem aged Alzheimer’s disease brains correlating with increasing tauopathy, it is important to decipher if tauopathy is underlying brain imaging results of atrophy in ASD/ID children. We concentrated on activity-dependent neuroprotective protein (ADNP), a prevalent autism gene. The unique availability of multiple postmortem brain sections of a 7-year-old male, heterozygous for ADNP de novo mutation c.2244Adup/p.His559Glnfs*3 allowed exploration of tauopathy, reflecting on a general unexplored mechanism. The tested subject exhibited autism, fine motor delays, severe intellectual disability and seizures. The patient died after multiple organ failure following liver transplantation. To compare to other ADNP syndrome mutations, immortalized lymphoblastoid cell lines from three different patients (including ADNP p.Arg216*, p.Lys408Valfs*31, and p.Tyr719* heterozygous dominant mutations) and a control were subjected to RNA-seq. Immunohistochemistry, high-throughput gene expression profiles in numerous postmortem tissues followed. Comparisons to a control brain and to extensive datasets were used. Live cell imaging investigated Tau-microtubule interaction, protecting against tauopathy. Extensive child brain tauopathy paralleled by multiple gene expression changes was discovered. Tauopathy was explained by direct mutation effects on Tau-microtubule interaction and correction by the ADNP active snippet NAP. Significant pathway changes (empirical P value < 0.05) included over 100 genes encompassing neuroactive ligand–receptor and cytokine–cytokine receptor interaction, MAPK and calcium signaling, axon guidance and Wnt signaling pathways. Changes were also seen in steroid biosynthesis genes, suggesting sex differences. Selecting the most affected genes by the ADNP mutations for gene expression analysis, in multiple postmortem tissues, identified Tau (MAPT)-gene-related expression changes compared with extensive normal gene expression (RNA-seq) databases. ADNP showed relatively reduced expression in the ADNP syndrome cerebellum, which was also observed for 25 additional genes (representing >50% of the tested genes), including NLGN1, NLGN2, PAX6, SMARCA4, and SNAP25, converging on nervous system development and tauopathy. NAP provided protection against mutated ADNP disrupted Tau-microtubule association. In conclusion, tauopathy may explain brain-imaging findings in ADNP syndrome children and may provide a new direction for the development of tauopathy protecting drug candidates like NAP in ASD/ID.

Abstract B49: Effects of exercise on ovarian cancer initiation and progression

Abstract Epidemiology studies support a strong association between physical activity and lower risk of cancer. Exercise is a promising nonpharmacologic strategy in preventing cancer and mitigating adverse effects of cancer and anticancer therapies. However, we have not been able to optimize the efficacy of exercise training as an anticancer intervention due to the lack of knowledge regarding the biologic mechanisms of action, the effective doses, and the biomarkers for predicting and monitoring responses of exercise-based intervention. Our objective is to utilize mouse models to determine the effects and underlying mechanisms of exercise on ovarian cancer initiation and progression. C57BL/6 mice ran on a treadmill for 45min daily to mimic human exercise activity. The control groups were placed on treadmill for 45min daily. After a month of this exercise regiment, both groups were injected with cancer cells derived from ovarian tumors of Dicer-/-; Pten-/-; Tp53R172H mice. Tumor progression was monitored through IVIS imaging system. Blood and peritoneal fluid samples were tested for cytokine levels. Tissue samples were collected and gene expression levels were quantified via qPCR. Peritoneal macrophages were isolated after acute exercise and were used in flow cytometry analysis or cocultured with cancer cells. Our model resembled the biologic changes of exercise in human. Eight-week treadmill-running exercise suppressed early tumor formation and tumor spreading. Exercise altered visceral fat tissue gene expression profile, which may inhibit cancer-induced cachexia and metabolic imbalance. In addition, one-hour exercise induced the acute proinflammatory activation of peritoneal macrophages. Coculture of peritoneal macrophages and PBMC (peripheral blood mononuclear cells) or NK (natural killer) cells from the exercise group and cancer cells reduced survival of cancer cells. Chronic and acute exercise can both suppress ovarian cancer tumorigenesis in mouse models. The underlying mechanisms involve enhancing anticancer immune system responses and adjusting metabolic balance. More research is needed to determine the specific mechanisms by which chronic and acute exercise affects ovarian cancer. Citation Format: Fangfang Bi, Madeline Morrisson, Sarah Cady, Alexandra Cerchia, Kevin Yang, Ivy Ling, Yang Yang-Hartwich. Effects of exercise on ovarian cancer initiation and progression [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B49.

Dynamic transcriptome analysis unveils key proresolving factors of chronic inflammatory arthritis.

Despite recent advances in understanding chronic inflammation remission, global analyses have not been explored to systematically discover genes or pathways underlying the resolution dynamics of chronic inflammatory diseases. Here, we performed time-course gene expression profiling of mouse synovial tissues along progression and resolution of collagen-induced arthritis (CIA) and identified genes associated with inflammation resolution. Through network analysis of these genes, we predicted 3 key secretory factors responsible for the resolution of CIA: Itgb1, Rps3, and Ywhaz. These factors were predominantly expressed by Tregs and antiinflammatory M2 macrophages, suppressing production of proinflammatory cytokines. In particular, Ywhaz was elevated in the sera of mice with arthritis resolution and in the urine of rheumatoid arthritis (RA) patients with good therapeutic responses. Moreover, adenovirus-mediated transfer of the Ywhaz gene to the affected joints substantially inhibited arthritis progression in mice with CIA and suppressed expression of proinflammatory cytokines in joint tissues, lymph nodes, and spleens, suggesting Ywhaz is an excellent target for RA therapy. Therefore, our comprehensive analysis of dynamic synovial transcriptomes provides previously unidentified antiarthritic genes, Itgb1, Rps3, and Ywhaz, which can serve as molecular markers to predict disease remission, as well as therapeutic targets for chronic inflammatory arthritis.

Physiological and genome-wide RNA-sequencing analyses identify candidate genes in a nitrogen-use efficient potato cv. Kufri Gaurav

Nitrogen (N) is an important nutrient for plant growth. However, its excess application leads to environmental damage. Hence, improving nitrogen use efficiency (NUE) of plant is one of the plausible options to solve the problems. Aim of this study was to identify candidate genes involved in enhancing NUE in potato cv. Kufri Gaurav (N efficient). Plants were grown in aeroponic with two contrasting N regimes (low N: 0.75 mM, and high N: 7.5 mM). Higher NUE in Kufri Gaurav was observed in low N based on the parameters like NUE, NUpE (N uptake efficiency), NUtE (N utilization efficiency) and AgNUE (agronomic NUE). Further, global gene expression profiles in root, leaf and stolon tissues were analyzed by RNA-sequencing using Ion Proton™ System. Quality data (≥Q20) of 2.04–2.73 Gb per sample were mapped with the potato genome. Statistically significant (P ≤ 0.05) differentially expressed genes (DEGs) were identified such as 176 (up-regulated) and 30 (down-regulated) in leaves, 39 (up-regulated) and 105 (down-regulated) in roots, and 81 (up-regulated) and 694 (down-regulated) in stolons. The gene ontology (GO) terms like metabolic process, cellular process and catalytic activity were predominant. Our RT-qPCR analysis confirmed the gene expression profiles of RNA-seq. Overall, we identified candidate genes associated with improving NUE such as superoxide dismutase, GDSL esterase lipase, probable phosphatase 2C, high affinity nitrate transporters, sugar transporter, proline rich proteins, transcription factors (VQ motif, SPX domain, bHLH) etc. Our findings suggest that these candidate genes probably play crucial roles in enhancing NUE in potato.

1952-P: Vertical Sleeve Gastrectomy Induces Distinctive Gene Expression Changes in Glucose-Utilizing Peripheral Organs

Vertical sleeve gastrectomy (VSG) improves hyperglycemia and can achieve high rate of diabetes remission. To elucidate the molecular mechanism of VSG, we performed transcriptomic analysis of liver, fat, and muscle tissues in VSG mice compared to both sham and pair-fed sham controls. C57BL/6 mice fed high fat diet were randomly assigned to sham or VSG surgery. Sham-operated mice were fed ad libitum (Sham group) or pair-fed (Sham-PF group) matching their food intake to VSG-operated mice. Body weight, food intake, glucose and insulin tolerance were measured. Comparative transcriptomic analysis of liver, epididymal fat, and soleus muscle using RNA sequencing was performed. VSG decreased body weight and maintained the reduced body weight during the whole study period (up to 8 weeks after surgery). However, food intake was only reduced during the first 2 weeks after surgery in VSG than sham group. Glucose tolerance was improved by VSG after oral glucose load, but this improvement was attenuated after intraperitoneal glucose load. In addition, VSG increased insulin sensitivity than both Sham and Sham-PF group. Clustering and principal component analysis of the gene expression profiles of liver and adipose tissue revealed that Sham-PF was closer to Sham than VSG. The number of DEG was larger in comparison between VSG vs. Sham-PF than that between Sham-PF vs. Sham. The gene expression profile of muscle was not distinctive among the three groups. In pathway analysis, immune response was the common pathway enriched in all three tissues of VSG compared to Sham-PF. These results suggest that VSG induces organ specific changes of gene expression profile in both weight-loss dependent and independent ways. Interestingly, weight-loss independent changes were more robust than weight-loss dependent changes, which suggests that the improvement of hyperglycemia may be induced not only by weight-loss dependent mechanisms, but also by weight-loss independent mechanisms of VSG. Disclosure C. Ahn: None. S. Moon: None. Y. Cho: None. Funding Korean Ministry of Health and Welfare (HI14C1277)

Inhibition of EPS8L3 suppresses liver cancer progression and enhances efficacy of sorafenib treatment

BackgroundLiver cancer is a devastating disease that has second highest cancer mortality rate worldwide. Although surgical resection or liver transplantation sometimes cures early stage liver cancer, few therapeutic options are available for advanced-stage liver cancer, highlighting the importance of a better understanding of the disease to find novel therapeutic targets. MethodsFirstly, clinical features of EPS8L3 on liver cancer RNA-seq dataset of The Cancer Genome Atlas (TCGA) database was analyzed, including gene expression levels in tumor tissues in comparison with the normal tissues as well as the patients’ OS. To confirm the candidate genes, we used short hairpin RNA (shRNA) to knock down the gene and quantify the cell proliferation, apoptosis, and migration. Then micro-array analysis was did to investigate the intracellular mechanisms of EPS8L3. Moreover, to gain further insights into the translational value of the findings, we treated the liver cancer cells with Sorafenib after knocking down the candidate gene, in order to interrogate the combinatorial inhibitory effects on cell metabolism. ResultsAs a result, by comparing gene expression profiles of normal liver and cancerous tissues, we find that epidermal growth factor receptor kinase substrate 8-like protein 3 (EPS8L3), a gene with unknown function, is upregulated in liver cancer, and is associated with poor prognosis. Further gene set analyses on liver cancer cells revealed that EPS8L3 is pertinent to cell division and proliferation. Indeed, knocking down EPS8L3 inhibits cell proliferation and migration, and triggers apoptosis in vitro. Additionally, when inoculated into mice, EPS8L3 knocked down cells exhibit slower growth rate. Moreover, EPS8L3 expression can substantially increase the efficacy of low dosage of Sorafenib treatment. Furthermore, the results of immunohistochemical staining of 90 paired liver cancer and adjacent normal samples demonstrated high expression of EPS8L3 yields poor prognosis in Chinese liver cancer patients. ConclusionsCollectively, our results suggest that EPS8L3 has pivotal oncogenic functions in liver cancer and we propose that EPS8L3 could be a potential therapeutic target to treat liver cancer.

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in wounding-response, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stress-responsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.

Maternal Protein Restriction Altered Insulin Resistance and Inflammation-Associated Gene Expression in Adipose Tissue of Young Adult Mouse Offspring in Response to a High-Fat Diet.

Maternal protein restriction is associated with increased risk of insulin resistance and inflammation in adulthood offspring. Here, we investigated whether maternal protein restriction could alter the risk of metabolic syndrome in postweaning high-fat (HF)-diet-challenged offspring, with focus on epididymal adipose tissue gene expression profile. Female ICR mice were fed a control (C) or a low-protein (LP) diet for two weeks before mating and throughout gestation and lactation, and their male offspring were fed an HF diet for 22 weeks (C/HF and LP/HF groups). A subset of offspring of control dams was fed a low-fat control diet (C/C group). In response to postweaning HF diet, serum insulin level and the homeostasis model assessment of insulin resistance (HOMA-IR) were increased in control offspring. Maternal LP diet decreased HOMA-IR and adipose tissue inflammation, and increased serum adiponectin level in the HF-diet-challenged offspring. Accordingly, functional analysis revealed that differentially expressed genes (DEGs) enriched in cytokine production were downregulated in the LP/HF group compared to the C/HF group. We also observed the several annotated gene ontology terms associated with innate immunity and phagocytosis in down-regulated DEGs between LP/HF and C/C groups. In conclusion, maternal protein restriction alleviated insulin resistance and inflammation in young offspring mice fed a HF diet but may impair development of immune system in offspring.

Gamma-Aminobutyric Acid Increases Erythropoietin by Activation of Citrate Cycle and Stimulation of Hypoxia-Inducible Factors Expression in Rats.

Erythropoietin (EPO) is the primary regulator of erythropoiesis in the mammalian fetus and adult. Deficiency of EPO induces anemia. In this study, we investigated the effect of gamma-aminobutyric acid (GABA) on serum EPO levels and erythropoiesis in rats. Expression levels of Epo-related genes were measured by quantitative real-time PCR (qPCR) and expression of Epo and Epo receptor (Epor) proteins were measured by immunohistochemistry. The gene and protein expression profiles of kidney tissue in GABA-treated rats were evaluated by ribonucleic acid (RNA) sequencing and two-dimensional electrophoresis (2-DE), respectively. GABA significantly increased serum EPO levels and expression levels of Epo and Epor. GABA increased expression levels of hypoxia-inducible factor (Hif)-1 and Hif-2. Seven proteins with expression levels showing >2-fold change were identified by 2-DE followed by MALDI-TOF MS in GABA-treated rat kidney. The top KEGG pathway from the identified proteins was the tricarboxylic acid cycle, and nicotinamide adenine dinucleotide (NADH) dehydrogenase, succinate dehydrogenase, and isocitrate dehydrogenase were identified as key proteins. GABA treatment significantly increased ATP levels and NADH dehydrogenase activity in a dose-dependent manner. In conclusion, GABA shows a new physiological role in EPO production, and it can thus can contribute to the prevention of anemia when used alone or in combination with other anemia treating drugs.

Blood-based multi-tissue gene expression inference with Bayesian ridge regression

Gene expression profiling is widely used in basic and cancer research but still not feasible in many clinical applications because tissues, such as brain samples, are difficult and not ethnical to collect. Gene expression in uncollected tissues can be computationally inferred using genotype and expression quantitative trait loci. No methods can infer unmeasured gene expression of multiple tissues with single tissue gene expression profile as input. Here, we present a Bayesian ridge regression-based method (B-GEX) to infer gene expression profiles of multiple tissues from blood gene expression profile. For each gene in a tissue, a low-dimensional feature vector was extracted from whole blood gene expression profile by feature selection. We used GTEx RNAseq data of 16 tissues to train inference models to capture the cross-tissue expression correlations between each target gene in a tissue and its preselected feature genes in peripheral blood. We compared B-GEX with least square regression, LASSO regression and ridge regression. B-GEX outperforms the other three models in most tissues in terms of mean absolute error, Pearson correlation coefficient and root-mean-squared error. Moreover, B-GEX infers expression level of tissue-specific genes as well as those of non-tissue-specific genes in all tissues. Unlike previous methods, which require genomic features or gene expression profiles of multiple tissues, our model only requires whole blood expression profile as input. B-GEX helps gain insights into gene expressions of uncollected tissues from more accessible data of blood. B-GEX is available at https://github.com/xuwenjian85/B-GEX. Supplementary data are available at Bioinformatics online.